8YUS
E. coli 70S ribosome complexed with P.putida tRNAIle2 and A(F)4 mRNA
This is a non-PDB format compatible entry.
Summary for 8YUS
| Entry DOI | 10.2210/pdb8yus/pdb |
| EMDB information | 39581 |
| Descriptor | 16S rRNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... (56 entities in total) |
| Functional Keywords | trna modification, decoding, ribosome |
| Biological source | Escherichia coli More |
| Total number of polymer chains | 55 |
| Total formula weight | 2209018.48 |
| Authors | Akiyama, N.,Ishiguro, K.,Shirouzu, M.,Suzuki, T. (deposition date: 2024-03-27, release date: 2024-11-06) |
| Primary citation | Miyauchi, K.,Kimura, S.,Akiyama, N.,Inoue, K.,Ishiguro, K.,Vu, T.S.,Srisuknimit, V.,Koyama, K.,Hayashi, G.,Soma, A.,Nagao, A.,Shirouzu, M.,Okamoto, A.,Waldor, M.K.,Suzuki, T. A tRNA modification with aminovaleramide facilitates AUA decoding in protein synthesis. Nat.Chem.Biol., 2024 Cited by PubMed Abstract: Modified tRNA anticodons are critical for proper mRNA translation during protein synthesis. It is generally thought that almost all bacterial tRNAs use a modified cytidine-lysidine (L)-at the first position (34) of the anticodon to decipher the AUA codon as isoleucine (Ile). Here we report that tRNAs from plant organelles and a subset of bacteria contain a new cytidine derivative, designated 2-aminovaleramididine (avaC). Like L34, avaC34 governs both Ile-charging ability and AUA decoding. Cryo-electron microscopy structural analyses revealed molecular details of codon recognition by avaC34 with a specific interaction between its terminal amide group and an mRNA residue 3'-adjacent to the AUA codon. These findings reveal the evolutionary variation of an essential tRNA modification and demonstrate the molecular basis of AUA decoding mediated by a unique tRNA modification. PubMed: 39300229DOI: 10.1038/s41589-024-01726-x PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.43 Å) |
Structure validation
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